|
| Status |
Public on Jul 12, 2017 |
| Title |
BPH114BE |
| Sample type |
SRA |
| |
|
| Source name |
Human prostate basal epithelia
|
| Organism |
Homo sapiens |
| Characteristics |
phenotype: non-BCH
facs ab profile: CD326+/CD49fHI/CD26-
|
| Treatment protocol |
Fresh surgical tissue samples were transported in ice-cold saline and immediately processed for an overnight enzymatic digestion into single cells at 37ºC. Single cells were flow sorted to isolate basal epithelia (CD326+/CD49fHI/CD26-).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from 500K FACS-purified basal cells was extracted using RNEasy micro columns (Qiagen). RNA quality and quantity were measured by a Bioanalyzer and NanoDrop.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Basal Epithelia from Tissue without Basal Cell Hyperplasia
114B
|
| Data processing |
Illumina's RTA version 1.18.66.3 was used for basecalling followed by bcl2fastq2 version 2.17.1.14 to generate fastq files.
Reads were trimmed using Trimmomatic version 0.32.
Reads were mapped to GRCh37 using TopHat version 2.1.12, with Bowtie2 version 2.2.3).
Mapped reads were filtered using SAMtools version 0.1.19 to remove those with a quality score MAPQ less than 10.
Quality-filtered mapped reads were quantified using Cufflinks' (version 2.2.1) CuffQuant and CuffNorm to generate FPKM.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Jun 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Gervaise H. Henry |
| E-mail(s) |
gervaise.henry@utsouthwestern.edu
|
| Phone |
2146480497
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Urology
|
| Lab |
Strand Lab
|
| Street address |
5323 Harry Hines Blvd, Mail Code:9110
|
| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE99824 |
Molecular pathogenesis of human prostate basal cell hyperplasia reveals a keratinocyte metaplasia |
|
| Relations |
| BioSample |
SAMN07206296 |
| SRA |
SRX2896435 |
